Modified "Cytosine becomes thymine" by CFCF - Own work. Licensed under CC BY-SA 3.0 via Wikimedia Commons.
9 September 2015
Modified "Cytosine becomes thymine" by CFCF - Own work. Licensed under CC BY-SA 3.0 via Wikimedia Commons.
http://episona.com/wp-content/uploads/2014/01/Agouti-Mouse-1024x802.jpg
Figure S7.1C, Integrated genomic analyses of ovarian carcinoma, TCGA, doi:10.1038/nature10166
Adapted from Krueger, F., et al., Nat. Methods 9, 145–151 (2012).
Going to focus on contemporary high-throughput assays based on sodium bisulfite treatment of DNA
Based on an enrichment/pulldown of methylated DNA and/or restriction enzymes
Most assay-specific:
Somewhere in between:
Less assay-specific:
Bioconductor 3.1 packages (based on DNAMethylation BiocViews):
I can't tell you everything
Will tell you:
.idat filesread.450k(), read.450k.exp(), read.450k.sheet()readTCGA()readGEORawFile()See:
detectionP()preprocessRaw(), preprocessIllumina(), preprocessQuantile(), preprocessNoob(), preprocessSWAN(), preprocessFunnorm()dropLociWithSnps()\(\beta = \frac{M}{M + U + 100} \in [0, 1]\)
\(\mathcal{M} = \log(\frac{M + 1}{U + 1}) \in [-\infty, \infty]\)
"We recommend using the \(\mathcal{M}\)-value method for conducting differential methylation analysis and including the \(\beta\)-value statistics when reporting the results to investigators." (Du, P. et al. BMC Bioinformatics 11, 587 (2010))
minfi::dmpFinder()minfi::blockFinder() with the bumphunter::bumphunter() backendmissMethyl::varFit, missMethyl::topVar() based on limmaSingle-base resolution data of cytosine methylation
Still being figured out …
There are also non-R/Bioconductor options
chr pos M U chr7 666 13 2 chr7 685 12 0
What you can do with a microarray plus more
Cartoon (see e.g., bsseq::BSmooth() for a proper implementation)
Cartoon (see e.g., bsseq::BSmooth() for a proper implementation)
Cartoon (see e.g., bsseq::BSmooth.tstat() and bsseq::dmrFinder() for a proper implementation)
Cartoon (see e.g., bsseq::BSmooth.tstat() and bsseq::dmrFinder() for a proper implementation)
Yes, they affect DNA methylation data!
RUVadj() and RUVfit() specific to 450k data.Check out AnnotationHub
WARNING: The remaining 'slides' are notes and are not part of the presentation